Abstract

Background

Virtual microscopy includes digitisation of histology slides and the use of computer
technologies for complex investigation of diseases such as cancer. However, automated
image analysis, or website publishing of such digital images, is hampered by their
large file sizes.

Results

We have developed two Java based open source tools: Snapshot Creator and NDPI-Splitter.
Snapshot Creator converts a portion of a large digital slide into a desired quality
JPEG image. The image is linked to the patient’s clinical and treatment information
in a customised open source cancer data management software (Caisis) in use at the
Australian Breast Cancer Tissue Bank (ABCTB) and then published on the ABCTB website
(http://www.abctb.org.auwebcite) using Deep Zoom open source technology. Using the ABCTB online search engine, digital
images can be searched by defining various criteria such as cancer type, or biomarkers
expressed. NDPI-Splitter splits a large image file into smaller sections of TIFF images
so that they can be easily analysed by image analysis software such as Metamorph or
Matlab. NDPI-Splitter also has the capacity to filter out empty images.

Conclusions

Snapshot Creator and NDPI-Splitter are novel open source Java tools. They convert
digital slides into files of smaller size for further processing. In conjunction with
other open source tools such as Deep Zoom and Caisis, this suite of tools is used
for the management and archiving of digital microscopy images, enabling digitised
images to be explored and zoomed online. Our online image repository also has the
capacity to be used as a teaching resource. These tools also enable large files to
be sectioned for image analysis.